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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ARABIDOPSIS RECEPTOR KINASE HAESA IN COMPLEX WITH THE PEPTIDE HORMONE IDA AND THE CO-RECEPTOR SERK1
 
Authors :  J. Santiago, M. Hothorn
Date :  24 Mar 16  (Deposition) - 20 Apr 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.43
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Membrane Receptor Kinase, Peptide Hormone Receptor, Signaling Complex, Plant Development, Organ Shedding, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Santiago, B. Brandt, M. Wildhagen, U. Hohmann, L. A. Hothorn, M. A. Butenko, M. Hothorn
Mechanistic Insight Into A Peptide Hormone Signaling Comple Mediating Floral Organ Abscission.
Elife V. 5 2016
PubMed-ID: 27058169  |  Reference-DOI: 10.7554/ELIFE.15075

(-) Compounds

Molecule 1 - RECEPTOR-LIKE PROTEIN KINASE 5
    Chains: A
    EC Number: 2.7.10.1, 2.7.11.1
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: BTI38
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PBAC3MOD
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: ECTODOMAIN, RESIDUES 20-620
    Gene: RLK5, HAE, AT4G28490, F21O9.180
    Organ: FLOWER
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: PROTEIN HAESA
    Tissue: ABCSISSION
 
Molecule 2 - PROTEIN IDA
    Chains: B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PBAC3MOD
    Expression System Strain: BTI38
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 56-69
    Gene: IDA, AT1G68765, F14K14
    Organ: FLOWER
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: PROTEIN INFLORESCENCE DEFICIENT IN ABSCISSION
    Tissue: ABSCISSION ZONE
 
Molecule 3 - SOMATIC EMBRYOGENESIS RECEPTOR KINASE 1
    Chains: C
    EC Number: 2.7.10.1, 2.7.11.1
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PBAC3MOD
    Expression System Strain: BTI38
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Gene: SERK1, AT1G71830, F14O23.21, F14O23_24
    Organ: FLOWER
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Other Details: N115D AND N163Q
    Synonym: ATSERK1,SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE 1
    Tissue: ABSCISSION ZONE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2HYP1Mod. Amino Acid4-HYDROXYPROLINE
3NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:193binding site for residue EDO A 711
02AC2SOFTWARETYR A:383 , HIS B:68binding site for residue EDO A 712
03AC3SOFTWARESER A:74 , MET A:76 , TYR A:97 , ASN A:98 , HOH A:828binding site for Poly-Saccharide residues NAG A 701 through NAG A 702 bound to ASN A 98
04AC4SOFTWAREASN A:102binding site for Mono-Saccharide NAG A 703 bound to ASN A 102
05AC5SOFTWAREASN A:150 , ARG A:614 , LYS A:615 , HOH A:844 , TYR B:56binding site for Poly-Saccharide residues NAG A 704 through NAG A 705 bound to ASN A 150
06AC6SOFTWAREPHE A:245 , ASN A:269 , MET A:293 , GLU A:316 , ASP A:610 , HOH A:882 , ASN C:27binding site for Poly-Saccharide residues NAG A 706 through NAG A 707 bound to ASN A 269
07AC7SOFTWARETHR A:257 , ASN A:282binding site for Mono-Saccharide NAG A 708 bound to ASN A 282
08AC8SOFTWARESER A:555 , SER A:556 , ASN A:576 , TYR A:579 , HIS A:597binding site for Poly-Saccharide residues NAG A 709 through NAG A 710 bound to ASN A 576
09AC9SOFTWARELEU C:126 , ASN C:150 , ASN C:174 , HOH C:434binding site for Mono-Saccharide NAG C 301 bound to ASN C 150
10AD1SOFTWARETHR C:162 , GLN C:163 , ASN C:184binding site for Mono-Saccharide NAG C 302 bound to ASN C 184

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:54 -A:61
2A:86 -A:113
3A:376 -A:402
4A:606 -A:613
5C:58 -C:65
6C:202 -C:210

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5IYX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IYX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IYX)

(-) Exons   (0, 0)

(no "Exon" information available for 5IYX)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:596
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.................hhhhh..eee.....eeeee......ee..hhhhhhh....eee....ee....hhhhhh......eee......ee....hhhhhh....eee....ee....hhhhhhh....eee..........hhhhhhh....eee...........hhhhhhh....eee......ee..hhhhhhh....eee....ee....hhhhhhh....eee..........hhhhhhh....eee....................eee......ee..hhhhhhh....eee....eeeee............eee....eeee.............eee....eeee..hhhhhhh....eee....eeeee.hhhhhh.....eee....eeee..hhhhhhh....eee....eeeee.hhhhhhh....eee....eee...hhhhhhh....eee......ee.............eee....eeee..hhhhhhh....eee....eeee..hhhhhhh...eee....eeeee......hhhhhhhhh...eeeee....ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iyx A  21 LNQDATILRQAKLGLSDPAQSLSSWSDNNDVTPCKWLGVSCDATSNVVSVDLSSFMLVGPFPSILCHLPSLHSLSLYNNSINGSLSADDFDTCHNLISLDLSENLLVGSIPKSLPFNLPNLKFLEISGNNLSDTIPSSFGEFRKLESLNLAGNFLSGTIPASLGNVTTLKELKLAYNLFSPSQIPSQLGNLTELQVLWLAGCNLVGPIPPSLSRLTSLVNLDLTFNQLTGSIPSWITQLKTVEQIELFNNSFSGELPESMGNMTTLKRFDASMNKLTGKIPDNLNLLNLESLNLFENMLEGPLPESITRSKTLSELKLFNNRLTGVLPSQLGANSPLQYVDLSYNRFSGEIPANVCGEGKLEYLILIDNSFSGEISNNLGKCKSLTRVRLSNNKLSGQIPHGFWGLPRLSLLELSDNSFTGSIPKTIIGAKNLSNLRISKNRFSGSIPNEIGSLNGIIEISGAENDFSGEIPESLVKLKQLSRLDLSKNQLSGEIPRELRGWKNLNELNLANNHLSGEIPKEVGILPVLNYLDLSSNQFSGEIPLELQNLKLNVLNLSYNHLSGKIPPLYANKIYAHDFIGNPGLCVDLDGLCRKI 616
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610      


Chain B from PDB  Type:PROTEIN  Length:14
                                              
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 5iyx B  56 YVPIPPSApSKRHN  69
                                    65    
                                   64-HYP 


Chain C from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhee..............hhhhh..eee.....eeeee......ee..hhhhhhh....eee....eeeee.hhhhhhh....eee....eeee..hhhhhhh....eee....eeee..hhhhhhh....eee....eeeee...hhhhhhhhhhhh....eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5iyx C  26 ANLEGDALHTLRVTLVDPNNVLQSWDPTLVNPCTWFHVTCNNENSVIRVDLGNAELSGHLVPELGVLKNLQYLELYSNNITGPIPSNLGDLTNLVSLDLYLNSFSGPIPESLGKLSKLRFLRLNNNSLTGSIPMSLTQITTLQVLDLSNNRLSGSVPDNGSFSLFTPISFANNLDLCGPVTSHPCP 211
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5IYX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IYX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IYX)

(-) Gene Ontology  (36, 55)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        IDA_ARATH | Q8LAD7: 5ixq 5ixt
        RLK5_ARATH | P47735: 5ixo 5ixq 5ixt 5iyv
        SERK1_ARATH | Q94AG2: 4lsc 4lsx 4z64

(-) Related Entries Specified in the PDB File

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